Secrets and Mysteries
by SomeguyBehindAScreen
Summary: Secrets and Mysteries, This Journey is full of them. While on the next part of his journey to becoming a Pokemon Master, a dark force appears with plans of destruction... During his journey, he will meet familiar and new faces alike. Friends and foes. He will learn a lot, and not just from the school. This journey won't just be sunshine and rainbows under the Alolan Sun...


A couple months ago, the region of Kalos fought for not only their lives, but the world's as well. Team Flare had sought to destroy the current world and start anew. To do this, they collected a substance named "Mega Evolution Energy." The energy given off from Pokemon when they undergo an amazing transformation. Flare used this energy to take control of Zygarde, a Legendary Pokemon of the region. With its power, and the eventually second one they took control off brought devastation to Lumiose City. Eventually, a group of trainers, including the League finalists, Gym leaders, and Champion of Kalos, fought to save the region. Flare was defeated, but the energy seemingly had other plans. Taking a form almost identical to Zygarde 50%, the energy attempted to reach the Sundial. The Sundial gives off energy very similar to the energy of Mega Evolution. With that much power, the world would've been destroyed in an instant. Instead, brave heroes fought the monster and won the day. Without a core or a leader, the energy was sealed away by the Zygarde at full power.

But the power would not rest this time…

With aide of a Greninja, the Legendary Pokemon attempt to rid any remaining sources of the energy under Kalos. Together, perhaps the could destroy the source of energy and its roots and save the world once and for all.

Or maybe not.

 **Deep In The Forests Of Kalos**

 **A Few Months After The Events Of XYZ**

It had been months since he had left his trainer, his partner in battle. He would like if he ever said he didn't miss the boy, but bigger problems we're the concern at the moment. He knew this well.

This particular Pokemon, Greninja, is able to sense the energy deep below the Kalos region, making him the prime candidate to destroy the remains of Flare's horrible attack.

Greninja jumped tree to tree, branch to branch, almost as if silently gliding above the ground below. He moved quickly, searching for the next step in being able to reunite with his trainer.

On the ground below, The two Zygarde cores watched the Pokemon try to sense more of the Mega Evolution Energy.

One core was in its basic form, was named Squishy by a certain young girl and codenamed Z-1 by Team Flare. Z-2, as codenamed by Flare, remained in its 50% form, cautious of a sudden attack.

Soon enough, a root of energy emerged from the earth and Greninja quickly got to work. Doing this many times previously, he destroyed the root almost as if it was clockwork. Summoning Water Shurikens and cutting the horrible sight down to nothingness.

Surely, he had to be close to done. He had destroyed so many roots of energy already, the end must be near. Soon, he would be done, he would be able to leave and find his trainer once more. He had to be close to done, right?

 **You wish.**

Greninja paused as if it heard something. Almost as a whisper. Were him and the cores truly alone?

"Another root destroyed, surely there can't be many more. Surely we are searching for the last few." Z-1 spoke to Greninja telepathically.

"We would hope so, but Greninja is sensing more and more energy everyday. Hopefully it is just the last few appearing easier to you due to the lack of interference from others." Z-2 said trying to come up with a logical solution.

"Gren." Greninja said, agreeing.

"You know, part of me is curious of something." Z-1 started.

"And what is that?" Z-2 asked confused.

"Well. This reminds me of long ago. The energy seems very similar to the Negative Energy from the Ancient times." Z-1 explained.

"It has been ages. Why would it awaken once again, now of all times?" Z-2 asked.

"Perhaps Flare did more than harness Mega Evolution Energy, if the Energy corrupted…"

"It would become Negative Energy. But if Flare truly did awaken that force, wouldn't we know it by now?" Z-2 asked.

"Maybe not. It was powerful enough to control us. It even attempted a dash for the Sundial. If this is the same energy from then. Then it's getting stronger." Z-1 said in worry.

"Gren?" Greninja asked confused what the two meant. What had been awoken?

 _ **HahaHahAhahaHaHahAHa**_

A sinister laugh filled the forest, scary nearby Pokemon into hiding.

"This isn't good." Z-1 commented.

"Greninja!" Greninja said taking a battle stance.

The ground began to tremble as the ground stated to break a few feet away from the Pokemon.

Emerging from it came a root different from the others. Instead of taking its root form, it had pale bark and sprouted red leaves from its branches.

"How odd. It became a small tree?" Z-2 pondered.

"Regardless, it must be destroyed." Z-1 said to Greninja.

"Gren!"

Greninja took its Water Shurikens and striked the tree with blow after blow. After the smoke settles, it revealed the tree still in tact, not a leaf disturbed.

"How peculiar." Z-1 commented.

"If it's going to be stubborn, then I'll aid you." Z-2 said in confidence, charging and then firing a Dragon Pulse at the tree.

Once again, not a scratch made.

"How is that possible?!" Z-2 said shocked.

"It isn't. That means…"Z-1 began."

The tree started to become engulfed in darkness. An energy leaking from the plant. The energy encased the tree, almost resembling a cocoon. It was almost as if it glew from the darkness surrounding it.

Soon the object started to change the shape.

 _ **HahaHahAhahaHaHahAHa**_

The same distorted and loud voice laughed.

Greninja wasn't sure what was going on, but whatever it was wasn't good.

The dark object that was now in place of the tree started to resemble almost a humans shape. More like one's shadow. Soon, two eyes appeared from it's head, Blood Red.

"Oh… it's been quite some time. Trapped in an eternal prison of nothingness. Eternal wasn't as long as it was made out to be." The figure laughed at the situation.

"You three have been quite troublesome. But it doesn't matter now. The roots did their job either way." It continued.

"Zygarde. Zygardes… You know it is quite confusing how to address the two of you. I mean, are you separate beings, one being… A bigger being divi- Oh what does it matter." It said cutting itself off. It then noticed Greninja still in his defensive position.

"Oh, you have a friend. Were the hundred of you cells not enough company?" It asked with a snicker.

"What are you doing here…" Z-2 asked the being. It clearly recognized it from somewhere.

"Do you really need to ask? After a few centuries I thinks about time I get back to it. Causing pain and suffering, destruction. Same old routine." It replied.

"You know what happened last time. None of that will happen." Z-1 said in confidence.

"Oh yes, what a tragedy that all was. But that's all in the past, this is a new start for red suited idiots we're so close. Almost did my job for me, but failed in the end due to 'the power of love and friendship'" it said in a mocking tone. "What a bore. Although, I must give some credit. They are the reason why I'm here now. Another chance at destruction that I won't let go to waste. Nothing will stop me this time." It said laughing once more.

"You seem awful confident in your plans." Z-2 commented.

"Why, yes, I am. Why not be? I was killed a very long time ago. The Hero is long dead. So what is there to for me to fear?" It asked almost as begging for an answer.

It then looked towards the Greninja with the Legendary, its energy…

"No way… So that's how it is." It spoke connecting dots.

"Seems the Hero doesn't stay dead. It's power lives on." It spoke sinisterly.

Z-1 and Z-2 reacted with surprise. They knew Greninja's transformation was special, but they would've never guessed that was it was.

Their only hope.

"Well, if you're here, surely your trainer is too. I can't wait to see what miserable excuse of a partner you chose Hero." It laughed evilly.

"Gren!" Greninja said with anger narrowing his eyes.

"So where is the man of the hour? I'll end this quick so he can get on with his afterlife. Let out battle COMMENCE!"

Silence was the only noise that came from the forest.

"Uh. LET OUR BATTLE COMMENCE!" It yelled.

No noise except for fleeing Pokemon from the monster.

Its eyes grew an even darker shade of red. "I said, **LET OUR BATTLE COMMENCE**!" It screamed, sending a shiver down Greninja's spine.

"Okay… Where are they? Being a Chicken or something? Ran home to mommy already?" It laughed.

"He's gone. He left Kalos a while ago. I have no idea where he could've gone. He could be anywhere." Z-1 explained to the being of energy.

"What? He's not here?" It said in disbelief.

"Gren." Greninja said confirming.

" **WHAT! THE GREAT BATTLE OF THE WORLD AND HE DOESN'T EVEN SHOW UP, THE NERVE-** " It yelled with eyes glowing dark red once again, quickly turning brighter once again with realization. "Then again..." It started, snickering.

"Why not seize opportunity. Why rush things? The last battle wasn't short, and that was a blast! Except for the outcome of course. Anyways." It continued,"If they won't come to me, I'll go to them." It then laughed maniacally. "Why not have some fun with my victim?"

Greninja had a good feeling he knew what it meant, he wasn't gonna let his trainer down again, not after last time.

Greninja took a fighting stance, against the being. "Gren!" He stated.

"Really? You wish to fight me without your trainer? I hope you don't expect aide from your friends. They can't help you." It explained to the Pokemon. Z-1 looked down ashamed. It was true.

"Fine. I need a good warm up after being dead for so long. Destroying you would be a good start." It chuckled, wickedness apparent.

"Make your move Hero. Don't disappoint me."

With the statement finished Greninja rushed at the being, using Cut to summon two icicle blades, the creature dodged Greninja's swipes with ease.

It retaliated striking Greninja with a dark blade of negative energy, similar to Greninja's Cut attack.

The force of the blast sent Greninja into a tree, indenting it. He was dazed, but not down.

The creature snickered, "Seriously? Cut?" Said it laughing once again.

Greninja, using the moment of distraction to strike at the being.

He jumped to his feet and combined two Water Shurikens creating one big one, sending it flying at his opponent with impressive power and speed.

As it approached, the creature did not move, instead it did the impossible. The being caught the Water Shurikens witch was still spinning with high velocity.

Greninja looked at the event in panic, just what was it up against?

With the Shuriken in hands, it muttered a single sentence to Greninja, "Nice try." With that, it sent the move flying towards Greninja, connecting before he could even react.

Once the smoke from the hit cleared, Greninja could be seen fainted in a small crater created from the impact of the hit. Trees destroyed in the path Greninja took flying backwards.

The cores looked over to their friend with worry. Maybe they couldn't defeat the being, but they could still help their friend. They rushed over to help its friend, as the being slowly faded away.

"Well, THAT was fun." It laughed. "Time to go search the world for your great hero of the world. Oh, and don't worry frog," It said menacingly, "I'll say hi for you..." it said as it disappeared.

Greninja thought of one thing as it blacked out, it had to find Ash.

And soon…

 _ **Pokemon: Secrets and Mysteries**_


End file.
